Secondary and Tertiary Structure in Proteins

Question 1

Genetic Code

Answer 1

How the sequence of DNA dictates the sequence of proteins - triplet code

Question 2

quaternary structure

Answer 2

• interactions between subunits

Question 3

all folding orders dictated by

Answer 3

primary sequence of the protein

Question 4

the major secondary structures in proteins

Answer 4

1. alpha-helix
2. beta-sheet
3. beta-turn
4. random coils

Question 5

structure and function

Answer 5

closely tied to one another

Question 6

determine the structure of proteins

Answer 6

• use X-ray crystalography

Question 7

X-ray crystallography

Answer 7

• proteins must be collected at high concentrations and crystallized
• crystals exposed to X-rays and diffracted by protein in a way determined by position of chemical bonds within the protein
• diffraction pattern produces 3D image of density of electrons within crystal to determine protein structure. q

Question 8

Linus Pauling’s solution of the alpha-helix

Answer 8

• contributed to structure of DNA - the way H bonds stabilize alpha-helices in proteins
• The Nature of the Chemical Bond
• proposed alpha-helix and beta-sheet
• establishes hydrophobic face that will interact with other proteins to form a leucine dimer
• proposed triple helix -wrong!

Question 9

alpha-helix

Answer 9

• hydrogen bonds between C=O and NH stabilize the helix
• one helical turn ~ 3.5 amino acids
• two turns = 7 amino acids
  
  • every 7th amino acid will have R-groups on the same face of the helix - important for protein interaction

Question 10

Beta-sheet

Answer 10

• hydrogen bonds between C=O and NH stabilize the B-sheet
• remaining C=O and NH can hydrogen bond with another B-sheeet creating B-pleated structures
• flattened sheet instead of helical structure

Question 11

anti-parallel

Answer 11

• amino group adjacent to carboxy group of next

- more stable and found more commonly

Question 12

parallel

Answer 12

• all amino termini in same direction

Question 13

ribbon structure

Answer 13

• idealized drawings of the tertiary structures of several globular proteins (secondary structures)
• coiled regions represent alpha helix and flat arrows indicate beta-structure

Question 14

Barrel structure

Answer 14

• another way of drawing alpha-helices

- alpha-helix between two beta-sheets

Question 15

Chou-Gasman table

Answer 15

• propensity of amino acids to form alpha-helix or beta-sheet based on proteins of known sequence and known secondary structure from x-ray crystallography

Question 16

most likely to be found in alpha-helix

Answer 16

• Glu
• Ala
• Leu

Question 17

least likely to be found in alpha-helix

Answer 17

• Pro

- Gly

Question 18

most likely to be found in beta-sheet

Answer 18

• Met
• Val
• Ile

Question 19

least likely to be found in beta-sheet

Answer 19

• Pro

- Glu

Question 20

Absolute helix breakers

Answer 20

• proline and glycine

Question 21

proline

Answer 21

• not in alpha-helix due to its structure

- no H bond because tied up in ring structure.

Question 22

Chou-Fasman Rules

Answer 22

• are used to PREDICT (not Determine) secondary structure in proteins.

Question 23

hydrophobic interactions and tertiary structure

Answer 23

• hydrophilic outside to interact with H2O

- hydrophobic inside to not react with H2O

Question 24

Hydropathy index

Answer 24

• help predict tertiary structure of protein also using sliding window approach

Question 25

Sliding window

Answer 25

• Consider 5 AA next to each other
  
  • average hydropathy index
  • plot
• slide down one AA

Question 26

Hydropathy plots

Answer 26

• done for whole length of protein
• help determine which regions are hydrophobic or hydrophilic in a given protein
• good sliding window of 9

Question 27

bars above 0

Answer 27

interior regions of the protein as determined by crystallography

Question 28

bars below 0

Answer 28

exterior region of the protein as determined by crystallography

Question 29

A reason why you might expect a hydrophobic portion of a protein to be on the outside of a protein rather than on the inside

Answer 29

• if a protein spans a membrane

- if a portion of the protein is involved in an INTERACTION with another macromolecule through hydrophobic interactions

Question 30

Homology modeling

Answer 30

• constructing a model of a protein based off known AA seq and known 3D seq of related protein with similar function
• identification of insect olfactory receptors after mammalian receptors identified

Question 31

hydropathy plots for evolutionary comparisons

Answer 31

• to identify functional homologues